PMC:7219429 / 8539-10044 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T37","span":{"begin":5,"end":16},"obj":"Body_part"},{"id":"T38","span":{"begin":48,"end":59},"obj":"Body_part"},{"id":"T39","span":{"begin":94,"end":104},"obj":"Body_part"},{"id":"T40","span":{"begin":155,"end":165},"obj":"Body_part"},{"id":"T41","span":{"begin":273,"end":284},"obj":"Body_part"},{"id":"T42","span":{"begin":525,"end":536},"obj":"Body_part"},{"id":"T43","span":{"begin":622,"end":624},"obj":"Body_part"},{"id":"T44","span":{"begin":866,"end":877},"obj":"Body_part"},{"id":"T45","span":{"begin":1000,"end":1012},"obj":"Body_part"},{"id":"T46","span":{"begin":1026,"end":1031},"obj":"Body_part"},{"id":"T47","span":{"begin":1198,"end":1205},"obj":"Body_part"},{"id":"T48","span":{"begin":1305,"end":1320},"obj":"Body_part"}],"attributes":[{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma82780"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma82780"},{"id":"A41","pred":"fma_id","subj":"T41","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A42","pred":"fma_id","subj":"T42","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A43","pred":"fma_id","subj":"T43","obj":"http://purl.org/sig/ont/fma/fma66599"},{"id":"A44","pred":"fma_id","subj":"T44","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A45","pred":"fma_id","subj":"T45","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A46","pred":"fma_id","subj":"T46","obj":"http://purl.org/sig/ont/fma/fma67264"},{"id":"A47","pred":"fma_id","subj":"T47","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A48","pred":"fma_id","subj":"T48","obj":"http://purl.org/sig/ont/fma/fma67906"}],"text":"2.3 Ganglioside GM1\nThe initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part. In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: 34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). The system was energy-minimized 6 times switching alternatively between runs using steepest descent gradients or Polak-Ribière conjugate gradients until convergence to machine precision [16]. The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. The whole system was optimized, merged with SARS-CoV-2 spike protein (chain A) and submitted to MD simulations with the same conditions as those used for the ATM-spike protein complex (50-ns run in triplicate). For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding lipids."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T36","span":{"begin":1181,"end":1189},"obj":"Disease"}],"attributes":[{"id":"A36","pred":"mondo_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"2.3 Ganglioside GM1\nThe initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part. In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: 34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). The system was energy-minimized 6 times switching alternatively between runs using steepest descent gradients or Polak-Ribière conjugate gradients until convergence to machine precision [16]. The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. The whole system was optimized, merged with SARS-CoV-2 spike protein (chain A) and submitted to MD simulations with the same conditions as those used for the ATM-spike protein complex (50-ns run in triplicate). For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding lipids."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T81","span":{"begin":306,"end":314},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T82","span":{"begin":352,"end":353},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T83","span":{"begin":447,"end":455},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T84","span":{"begin":553,"end":554},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T85","span":{"begin":622,"end":624},"obj":"http://purl.obolibrary.org/obo/CLO_0001577"},{"id":"T86","span":{"begin":637,"end":638},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T87","span":{"begin":647,"end":648},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T88","span":{"begin":657,"end":658},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T89","span":{"begin":934,"end":936},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T90","span":{"begin":952,"end":953},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T91","span":{"begin":1016,"end":1017},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T92","span":{"begin":1037,"end":1045},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T93","span":{"begin":1213,"end":1214},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T94","span":{"begin":1233,"end":1235},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T95","span":{"begin":1305,"end":1320},"obj":"http://purl.obolibrary.org/obo/GO_0043234"},{"id":"T96","span":{"begin":1372,"end":1374},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T97","span":{"begin":1445,"end":1453},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"}],"text":"2.3 Ganglioside GM1\nThe initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part. In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: 34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). The system was energy-minimized 6 times switching alternatively between runs using steepest descent gradients or Polak-Ribière conjugate gradients until convergence to machine precision [16]. The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. The whole system was optimized, merged with SARS-CoV-2 spike protein (chain A) and submitted to MD simulations with the same conditions as those used for the ATM-spike protein complex (50-ns run in triplicate). For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding lipids."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T107","span":{"begin":5,"end":20},"obj":"Chemical"},{"id":"T108","span":{"begin":5,"end":16},"obj":"Chemical"},{"id":"T109","span":{"begin":17,"end":20},"obj":"Chemical"},{"id":"T111","span":{"begin":48,"end":63},"obj":"Chemical"},{"id":"T113","span":{"begin":48,"end":59},"obj":"Chemical"},{"id":"T114","span":{"begin":60,"end":63},"obj":"Chemical"},{"id":"T115","span":{"begin":94,"end":104},"obj":"Chemical"},{"id":"T116","span":{"begin":155,"end":165},"obj":"Chemical"},{"id":"T117","span":{"begin":273,"end":284},"obj":"Chemical"},{"id":"T118","span":{"begin":404,"end":407},"obj":"Chemical"},{"id":"T121","span":{"begin":408,"end":416},"obj":"Chemical"},{"id":"T122","span":{"begin":465,"end":473},"obj":"Chemical"},{"id":"T124","span":{"begin":502,"end":512},"obj":"Chemical"},{"id":"T125","span":{"begin":525,"end":536},"obj":"Chemical"},{"id":"T126","span":{"begin":587,"end":592},"obj":"Chemical"},{"id":"T127","span":{"begin":593,"end":602},"obj":"Chemical"},{"id":"T128","span":{"begin":866,"end":881},"obj":"Chemical"},{"id":"T130","span":{"begin":866,"end":877},"obj":"Chemical"},{"id":"T131","span":{"begin":878,"end":881},"obj":"Chemical"},{"id":"T132","span":{"begin":908,"end":917},"obj":"Chemical"},{"id":"T133","span":{"begin":934,"end":936},"obj":"Chemical"},{"id":"T134","span":{"begin":996,"end":999},"obj":"Chemical"},{"id":"T137","span":{"begin":1000,"end":1012},"obj":"Chemical"},{"id":"T138","span":{"begin":1026,"end":1031},"obj":"Chemical"},{"id":"T139","span":{"begin":1058,"end":1061},"obj":"Chemical"},{"id":"T142","span":{"begin":1062,"end":1071},"obj":"Chemical"},{"id":"T143","span":{"begin":1095,"end":1106},"obj":"Chemical"},{"id":"T144","span":{"begin":1115,"end":1128},"obj":"Chemical"},{"id":"T146","span":{"begin":1129,"end":1135},"obj":"Chemical"},{"id":"T147","span":{"begin":1198,"end":1205},"obj":"Chemical"},{"id":"T148","span":{"begin":1233,"end":1235},"obj":"Chemical"},{"id":"T149","span":{"begin":1295,"end":1298},"obj":"Chemical"},{"id":"T150","span":{"begin":1305,"end":1312},"obj":"Chemical"},{"id":"T151","span":{"begin":1372,"end":1374},"obj":"Chemical"},{"id":"T152","span":{"begin":1417,"end":1420},"obj":"Chemical"},{"id":"T155","span":{"begin":1498,"end":1504},"obj":"Chemical"}],"attributes":[{"id":"A107","pred":"chebi_id","subj":"T107","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A108","pred":"chebi_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/CHEBI_28892"},{"id":"A109","pred":"chebi_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A110","pred":"chebi_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A111","pred":"chebi_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A112","pred":"chebi_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A113","pred":"chebi_id","subj":"T113","obj":"http://purl.obolibrary.org/obo/CHEBI_28892"},{"id":"A114","pred":"chebi_id","subj":"T114","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A115","pred":"chebi_id","subj":"T115","obj":"http://purl.obolibrary.org/obo/CHEBI_33563"},{"id":"A116","pred":"chebi_id","subj":"T116","obj":"http://purl.obolibrary.org/obo/CHEBI_33563"},{"id":"A117","pred":"chebi_id","subj":"T117","obj":"http://purl.obolibrary.org/obo/CHEBI_28892"},{"id":"A118","pred":"chebi_id","subj":"T118","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A119","pred":"chebi_id","subj":"T118","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A120","pred":"chebi_id","subj":"T118","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A121","pred":"chebi_id","subj":"T121","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A122","pred":"chebi_id","subj":"T122","obj":"http://purl.obolibrary.org/obo/CHEBI_17761"},{"id":"A123","pred":"chebi_id","subj":"T122","obj":"http://purl.obolibrary.org/obo/CHEBI_52639"},{"id":"A124","pred":"chebi_id","subj":"T124","obj":"http://purl.obolibrary.org/obo/CHEBI_16646"},{"id":"A125","pred":"chebi_id","subj":"T125","obj":"http://purl.obolibrary.org/obo/CHEBI_28892"},{"id":"A126","pred":"chebi_id","subj":"T126","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A127","pred":"chebi_id","subj":"T127","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A128","pred":"chebi_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A129","pred":"chebi_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A130","pred":"chebi_id","subj":"T130","obj":"http://purl.obolibrary.org/obo/CHEBI_28892"},{"id":"A131","pred":"chebi_id","subj":"T131","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A132","pred":"chebi_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A133","pred":"chebi_id","subj":"T133","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"},{"id":"A134","pred":"chebi_id","subj":"T134","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A135","pred":"chebi_id","subj":"T134","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A136","pred":"chebi_id","subj":"T134","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A137","pred":"chebi_id","subj":"T137","obj":"http://purl.obolibrary.org/obo/CHEBI_28892"},{"id":"A138","pred":"chebi_id","subj":"T138","obj":"http://purl.obolibrary.org/obo/CHEBI_18059"},{"id":"A139","pred":"chebi_id","subj":"T139","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A140","pred":"chebi_id","subj":"T139","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A141","pred":"chebi_id","subj":"T139","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A142","pred":"chebi_id","subj":"T142","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A143","pred":"chebi_id","subj":"T143","obj":"http://purl.obolibrary.org/obo/CHEBI_16113"},{"id":"A144","pred":"chebi_id","subj":"T144","obj":"http://purl.obolibrary.org/obo/CHEBI_17636"},{"id":"A145","pred":"chebi_id","subj":"T144","obj":"http://purl.obolibrary.org/obo/CHEBI_64583"},{"id":"A146","pred":"chebi_id","subj":"T146","obj":"http://purl.obolibrary.org/obo/CHEBI_18059"},{"id":"A147","pred":"chebi_id","subj":"T147","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A148","pred":"chebi_id","subj":"T148","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"},{"id":"A149","pred":"chebi_id","subj":"T149","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"},{"id":"A150","pred":"chebi_id","subj":"T150","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A151","pred":"chebi_id","subj":"T151","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"},{"id":"A152","pred":"chebi_id","subj":"T152","obj":"http://purl.obolibrary.org/obo/CHEBI_18216"},{"id":"A153","pred":"chebi_id","subj":"T152","obj":"http://purl.obolibrary.org/obo/CHEBI_61048"},{"id":"A154","pred":"chebi_id","subj":"T152","obj":"http://purl.obolibrary.org/obo/CHEBI_73110"},{"id":"A155","pred":"chebi_id","subj":"T155","obj":"http://purl.obolibrary.org/obo/CHEBI_18059"}],"text":"2.3 Ganglioside GM1\nThe initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part. In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: 34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). The system was energy-minimized 6 times switching alternatively between runs using steepest descent gradients or Polak-Ribière conjugate gradients until convergence to machine precision [16]. The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. The whole system was optimized, merged with SARS-CoV-2 spike protein (chain A) and submitted to MD simulations with the same conditions as those used for the ATM-spike protein complex (50-ns run in triplicate). For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding lipids."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T3","span":{"begin":17,"end":20},"obj":"GlycoEpitope"},{"id":"T4","span":{"begin":60,"end":63},"obj":"GlycoEpitope"},{"id":"T5","span":{"begin":404,"end":407},"obj":"GlycoEpitope"},{"id":"T6","span":{"begin":878,"end":881},"obj":"GlycoEpitope"},{"id":"T7","span":{"begin":996,"end":999},"obj":"GlycoEpitope"},{"id":"T8","span":{"begin":1058,"end":1061},"obj":"GlycoEpitope"},{"id":"T9","span":{"begin":1417,"end":1420},"obj":"GlycoEpitope"}],"attributes":[{"id":"A3","pred":"glyco_epitope_db_id","subj":"T3","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A4","pred":"glyco_epitope_db_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A5","pred":"glyco_epitope_db_id","subj":"T5","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A6","pred":"glyco_epitope_db_id","subj":"T6","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A7","pred":"glyco_epitope_db_id","subj":"T7","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A8","pred":"glyco_epitope_db_id","subj":"T8","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A9","pred":"glyco_epitope_db_id","subj":"T9","obj":"http://www.glycoepitope.jp/epitopes/EP0050"}],"text":"2.3 Ganglioside GM1\nThe initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part. In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: 34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). The system was energy-minimized 6 times switching alternatively between runs using steepest descent gradients or Polak-Ribière conjugate gradients until convergence to machine precision [16]. The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. The whole system was optimized, merged with SARS-CoV-2 spike protein (chain A) and submitted to MD simulations with the same conditions as those used for the ATM-spike protein complex (50-ns run in triplicate). For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding lipids."}

{"project":"LitCovid-sentences","denotations":[{"id":"T65","span":{"begin":0,"end":20},"obj":"Sentence"},{"id":"T66","span":{"begin":21,"end":479},"obj":"Sentence"},{"id":"T67","span":{"begin":480,"end":615},"obj":"Sentence"},{"id":"T68","span":{"begin":616,"end":660},"obj":"Sentence"},{"id":"T69","span":{"begin":661,"end":852},"obj":"Sentence"},{"id":"T70","span":{"begin":853,"end":986},"obj":"Sentence"},{"id":"T71","span":{"begin":987,"end":1136},"obj":"Sentence"},{"id":"T72","span":{"begin":1137,"end":1347},"obj":"Sentence"},{"id":"T73","span":{"begin":1348,"end":1505},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.3 Ganglioside GM1\nThe initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part. In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: 34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). The system was energy-minimized 6 times switching alternatively between runs using steepest descent gradients or Polak-Ribière conjugate gradients until convergence to machine precision [16]. The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. The whole system was optimized, merged with SARS-CoV-2 spike protein (chain A) and submitted to MD simulations with the same conditions as those used for the ATM-spike protein complex (50-ns run in triplicate). For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding lipids."}

{"project":"LitCovid-PubTator","denotations":[{"id":"229","span":{"begin":5,"end":20},"obj":"Chemical"},{"id":"252","span":{"begin":1192,"end":1197},"obj":"Gene"},{"id":"253","span":{"begin":1181,"end":1191},"obj":"Species"},{"id":"254","span":{"begin":1299,"end":1304},"obj":"Gene"},{"id":"255","span":{"begin":48,"end":59},"obj":"Chemical"},{"id":"256","span":{"begin":60,"end":63},"obj":"Chemical"},{"id":"257","span":{"begin":273,"end":284},"obj":"Chemical"},{"id":"258","span":{"begin":404,"end":407},"obj":"Chemical"},{"id":"259","span":{"begin":465,"end":473},"obj":"Chemical"},{"id":"260","span":{"begin":502,"end":512},"obj":"Chemical"},{"id":"261","span":{"begin":525,"end":536},"obj":"Chemical"},{"id":"262","span":{"begin":587,"end":592},"obj":"Chemical"},{"id":"263","span":{"begin":866,"end":881},"obj":"Chemical"},{"id":"264","span":{"begin":901,"end":907},"obj":"Chemical"},{"id":"265","span":{"begin":996,"end":999},"obj":"Chemical"},{"id":"266","span":{"begin":1000,"end":1012},"obj":"Chemical"},{"id":"267","span":{"begin":1026,"end":1031},"obj":"Chemical"},{"id":"268","span":{"begin":1058,"end":1061},"obj":"Chemical"},{"id":"269","span":{"begin":1095,"end":1106},"obj":"Chemical"},{"id":"270","span":{"begin":1417,"end":1420},"obj":"Chemical"},{"id":"271","span":{"begin":1498,"end":1504},"obj":"Chemical"},{"id":"272","span":{"begin":225,"end":249},"obj":"Disease"},{"id":"273","span":{"begin":1115,"end":1135},"obj":"Disease"}],"attributes":[{"id":"A229","pred":"tao:has_database_id","subj":"229","obj":"MESH:D005677"},{"id":"A252","pred":"tao:has_database_id","subj":"252","obj":"Gene:43740568"},{"id":"A253","pred":"tao:has_database_id","subj":"253","obj":"Tax:2697049"},{"id":"A254","pred":"tao:has_database_id","subj":"254","obj":"Gene:43740568"},{"id":"A255","pred":"tao:has_database_id","subj":"255","obj":"MESH:D005732"},{"id":"A256","pred":"tao:has_database_id","subj":"256","obj":"MESH:D005677"},{"id":"A257","pred":"tao:has_database_id","subj":"257","obj":"MESH:D005732"},{"id":"A258","pred":"tao:has_database_id","subj":"258","obj":"MESH:D005677"},{"id":"A259","pred":"tao:has_database_id","subj":"259","obj":"MESH:D002518"},{"id":"A260","pred":"tao:has_database_id","subj":"260","obj":"MESH:D002241"},{"id":"A261","pred":"tao:has_database_id","subj":"261","obj":"MESH:D005732"},{"id":"A262","pred":"tao:has_database_id","subj":"262","obj":"MESH:D014867"},{"id":"A263","pred":"tao:has_database_id","subj":"263","obj":"MESH:D005677"},{"id":"A265","pred":"tao:has_database_id","subj":"265","obj":"MESH:D005677"},{"id":"A266","pred":"tao:has_database_id","subj":"266","obj":"MESH:D005732"},{"id":"A267","pred":"tao:has_database_id","subj":"267","obj":"MESH:D008055"},{"id":"A268","pred":"tao:has_database_id","subj":"268","obj":"MESH:D005677"},{"id":"A269","pred":"tao:has_database_id","subj":"269","obj":"MESH:D002784"},{"id":"A270","pred":"tao:has_database_id","subj":"270","obj":"MESH:D005677"},{"id":"A271","pred":"tao:has_database_id","subj":"271","obj":"MESH:D008055"},{"id":"A272","pred":"tao:has_database_id","subj":"272","obj":"MESH:C563601"},{"id":"A273","pred":"tao:has_database_id","subj":"273","obj":"MESH:D052536"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"2.3 Ganglioside GM1\nThe initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part. In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: 34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). The system was energy-minimized 6 times switching alternatively between runs using steepest descent gradients or Polak-Ribière conjugate gradients until convergence to machine precision [16]. The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. The whole system was optimized, merged with SARS-CoV-2 spike protein (chain A) and submitted to MD simulations with the same conditions as those used for the ATM-spike protein complex (50-ns run in triplicate). For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding lipids."}

{"project":"2_test","denotations":[{"id":"32405156-30525595-48151020","span":{"begin":114,"end":116},"obj":"30525595"},{"id":"32405156-31431523-48151021","span":{"begin":848,"end":850},"obj":"31431523"},{"id":"T58286","span":{"begin":114,"end":116},"obj":"30525595"},{"id":"T84656","span":{"begin":848,"end":850},"obj":"31431523"}],"text":"2.3 Ganglioside GM1\nThe initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part. In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: 34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). The system was energy-minimized 6 times switching alternatively between runs using steepest descent gradients or Polak-Ribière conjugate gradients until convergence to machine precision [16]. The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. The whole system was optimized, merged with SARS-CoV-2 spike protein (chain A) and submitted to MD simulations with the same conditions as those used for the ATM-spike protein complex (50-ns run in triplicate). For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding lipids."}